GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroB in Phaeobacter inhibens BS107

Align 3-dehydroquinate synthase, chloroplastic; EC 4.2.3.4 (characterized)
to candidate GFF1393 PGA1_c14100 3-dehydroquinate synthase AroB

Query= SwissProt::Q8RU74
         (442 letters)



>FitnessBrowser__Phaeo:GFF1393
          Length = 375

 Score =  279 bits (713), Expect = 1e-79
 Identities = 164/363 (45%), Positives = 216/363 (59%), Gaps = 9/363 (2%)

Query: 81  VEVDLGTRSYPIYIGAGLL-DQPDLLQRHIHGKRVLVVTNTTVAPLYLDKTISALTDGNP 139
           V V LG R+Y + IG  LL D    L   +   +V V+T+ TVA  +L+   + L     
Sbjct: 10  VHVALGERAYDVVIGPDLLADAGARLAPMLRRPKVAVLTDETVAAHHLEGLRAGLASAG- 68

Query: 140 NVTVESVILPDGEQFKNMETLMKVFDKAIESRLDRRCTFVALGGGVIGDMCGYAAASYLR 199
            + ++++ LP GE  K      +  +  +E +++R    +A GGGVIGD+ G+AAA   R
Sbjct: 69  -IEMDALALPPGESTKAWPQFSRAVEWLLEQKVERGDIVIAFGGGVIGDLAGFAAAVLRR 127

Query: 200 GVNFIQIPTTVMAQVDSSVGGKTGINHPLGKNMIGAFYQPQCVLIDTDTLNTLPDRELAS 259
           GV F+QIPT+++AQVDSSVGGKTGIN P GKN+IGAF+QP  VL DT  L TL  R+  +
Sbjct: 128 GVRFVQIPTSLLAQVDSSVGGKTGINAPQGKNLIGAFHQPSLVLADTALLGTLTPRDFLA 187

Query: 260 GLAEVIKYGLIRDAEFFEWQEQNMPLLLARDPTAFTYAIKRSCENKADVVSQDEKESGVR 319
           G  EV+KYGL+ DAEFFEW E   P L A D  A   A+ RS + KAD+V +DE E G R
Sbjct: 188 GYGEVVKYGLLGDAEFFEWLEAQGPALAAGDMAARVEAVTRSVQMKADIVVRDETEQGDR 247

Query: 320 ATLNLGHTFGHAVETGVGYG-QWLHGEAVAAGTVMAVDMSRRLGWIDDSLVQRVQKILQQ 378
           A LNLGHTF HA+E   GYG + LHGE VA G  +A ++S RLG        RV+  L+ 
Sbjct: 248 ALLNLGHTFCHALEAATGYGDRLLHGEGVAIGCALAFELSARLGLCSQEDPSRVRAHLKA 307

Query: 379 AKLPTS----PPETMTVEMFKSIMAVDKKVADGKLRLILLKGSLGNCVFTGDYDQKALDE 434
             + T     P E    E   ++M  DKKV DG+LR IL +G +G    TGD  Q A+ +
Sbjct: 308 MGMKTDLADIPGELPDAEALLALMGQDKKVVDGQLRFILARG-IGQAFVTGDVPQAAVLD 366

Query: 435 TLR 437
            LR
Sbjct: 367 VLR 369


Lambda     K      H
   0.318    0.133    0.385 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 357
Number of extensions: 11
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 442
Length of database: 375
Length adjustment: 31
Effective length of query: 411
Effective length of database: 344
Effective search space:   141384
Effective search space used:   141384
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate GFF1393 PGA1_c14100 (3-dehydroquinate synthase AroB)
to HMM TIGR01357 (aroB: 3-dehydroquinate synthase (EC 4.2.3.4))

Software error:

../bin/blast/fastacmd -i /tmp/list.13968.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.13968.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

For help, please send mail to the webmaster (help@microbesonline.org), giving this error message and the time and date of the error.